13 ats 2.0t auto ecu flash

Hello everyone, I just recievd my mpvi2 and looking to learn to self tune.
I have successfully read my vehicle and ive already flashed to turn off the cel due to catless downpipe.
I would like to make some slight changes in the shifting strategy of the vehicle to prevent it from lugging. I have made a few changes as to what mph it will upshot to see how i like it but my problem is that when i tried to flash the tcm I received a message that tcm not reporting or found i cant remember exactly the description .
What i did, go i to trans made some small changes then saved. I then proceeded to flash I changed ecu to do not write and I did the same for what i believe is the fpcm so I was only going to write to tcm. Is this the correct way or do i have to flash the ecu as well?
Many thanks in advanve,
Alex

Update I figured it out. Now low throttle cruise is way better as it is not completely lugging rhe motor down.